search

JuliaPy / PyPlot.jl

Plotting for Julia based on matplotlib.pyplot
https://github.com/JuliaPy/PyPlot.jl
MIT License
469 stars 85 forks source link

ResolvePackageNotFound error in Ubuntu/Linux #571

Open urlicht opened 11 months ago

urlicht commented 11 months ago

Not sure if it's a PyPlot-specific problem (could be caused by PyCall.jl or matplotlib itself I suppose)

Upon a fresh install of the latest release of PyCall (setting ENV["PYTHON"]="" to use a separate Julia miniconda environment), it fails to install certain packages, including matplotlib. Trying to install PyPlot.jl (or even manually activating the environment and performing conda install matplotlib) returns the following error:

Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.

ResolvePackageNotFound: 
  - conda==23.1.0

Reproducible across multiple Ubuntu machines running 18.04, 20.04, or 22.04

a2ray commented 11 months ago

Yes, I was absolutely unable to register a package update on GitHub/Registrator because of this. My solution was install matplolib through Conda.pip and then Conda.add, before pointing PyCall to Conda's python. It works now, see here for my solution within a build script. This needs to remain an open issue IMHO.

Alexander-Barth commented 11 months ago

Here is a reproducer using docker:

docker run -it   julia:1.9 /bin/bash
julia --eval 'using Pkg; Pkg.add("PyPlot");'
julia --eval 'using PyPlot'

I am wondering if it also affects non-Linux systems.

Full session ```bash $ docker run -it julia:1.9 /bin/bash Unable to find image 'julia:1.9' locally 1.9: Pulling from library/julia 648e0aadf75a: Pull complete f396ccff5916: Pull complete 5e8906fb6194: Pull complete f4f5ee390bc1: Pull complete Digest: sha256:fcb2a336582c4da45bd8a3ba97cc84f0556b89fbd103cda9ab305a591785c4ae Status: Downloaded newer image for julia:1.9 root@30d69add978b:/# julia --eval 'using Pkg; Pkg.add("PyPlot");' Installing known registries into `~/.julia` Updating registry at `~/.julia/registries/General.toml` Resolving package versions... Installed FixedPointNumbers ─ v0.8.4 Installed JSON ────────────── v0.21.4 Installed Preferences ─────── v1.4.0 Installed PyCall ──────────── v1.96.1 Installed ColorTypes ──────── v0.11.4 Installed Parsers ─────────── v2.7.2 Installed Conda ───────────── v1.9.1 Installed PrecompileTools ─── v1.1.2 Installed VersionParsing ──── v1.3.0 Installed PyPlot ──────────── v2.11.1 Installed Reexport ────────── v1.2.2 Installed LaTeXStrings ────── v1.3.0 Installed MacroTools ──────── v0.5.10 Installed Colors ──────────── v0.12.10 Updating `~/.julia/environments/v1.9/Project.toml` [d330b81b] + PyPlot v2.11.1 Updating `~/.julia/environments/v1.9/Manifest.toml` [3da002f7] + ColorTypes v0.11.4 [5ae59095] + Colors v0.12.10 [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.3.0 [1914dd2f] + MacroTools v0.5.10 [69de0a69] + Parsers v2.7.2 [aea7be01] + PrecompileTools v1.1.2 [21216c6a] + Preferences v1.4.0 [438e738f] + PyCall v1.96.1 [d330b81b] + PyPlot v2.11.1 [189a3867] + Reexport v1.2.2 [81def892] + VersionParsing v1.3.0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [b77e0a4c] + InteractiveUtils [b27032c2] + LibCURL v0.6.3 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.9.2 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays [10745b16] + Statistics v1.9.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.0.5+0 [deac9b47] + LibCURL_jll v7.84.0+0 [29816b5a] + LibSSH2_jll v1.10.2+0 [c8ffd9c3] + MbedTLS_jll v2.28.2+0 [14a3606d] + MozillaCACerts_jll v2022.10.11 [4536629a] + OpenBLAS_jll v0.3.21+4 [bea87d4a] + SuiteSparse_jll v5.10.1+6 [83775a58] + Zlib_jll v1.2.13+0 [8e850b90] + libblastrampoline_jll v5.8.0+0 [8e850ede] + nghttp2_jll v1.48.0+0 [3f19e933] + p7zip_jll v17.4.0+0 Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8c86e48c0db1564a1d49548d3515ced5d604c408/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/43d304ac6f0354755f1d60730ece8c499980f7ba/build.log` Precompiling project... 15 dependencies successfully precompiled in 42 seconds. 5 already precompiled. root@30d69add978b:/# julia --eval 'using PyPlot' [ Info: Installing matplotlib via the Conda matplotlib package... [ Info: Running `conda install -y matplotlib` in root environment Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. ResolvePackageNotFound: - conda==23.1.0 ERROR: InitError: failed process: Process(setenv(`/root/.julia/conda/3/x86_64/bin/conda install -y matplotlib`,["SHLVL=1", "PATH=/usr/local/julia/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", "PWD=/", "CONDA_PREFIX=/root/.julia/conda/3/x86_64", "JULIA_PATH=/usr/local/julia", "JULIA_GPG=3673DF529D9049477F76B37566E3C7DC03D6E495", "_=/usr/local/julia/bin/julia", "OPENBLAS_DEFAULT_NUM_THREADS=1", "JULIA_VERSION=1.9.2", "HOME=/root", "TERM=xterm", "CONDARC=/root/.julia/conda/3/x86_64/condarc-julia.yml", "OPENBLAS_MAIN_FREE=1", "HOSTNAME=30d69add978b", "PYTHONIOENCODING=UTF-8"]), ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] runconda(args::Cmd, env::String) @ Conda ~/.julia/packages/Conda/2lg2O/src/Conda.jl:128 [5] add(pkg::String, env::String; channel::String, satisfied_skip_solve::Bool, args::Cmd) @ Conda ~/.julia/packages/Conda/2lg2O/src/Conda.jl:256 [6] add (repeats 2 times) @ ~/.julia/packages/Conda/2lg2O/src/Conda.jl:239 [inlined] [7] pyimport_conda @ ~/.julia/packages/PyCall/ilqDX/src/PyCall.jl:721 [8] pyimport_conda @ ~/.julia/packages/PyCall/ilqDX/src/PyCall.jl:715 [inlined] [9] __init__() @ PyPlot ~/.julia/packages/PyPlot/H01LC/src/init.jl:173 [10] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1115 [11] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}) @ Base ./loading.jl:1061 [12] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128) @ Base ./loading.jl:1506 [13] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1783 [14] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [15] macro expansion @ ./loading.jl:1648 [inlined] [16] macro expansion @ ./lock.jl:267 [inlined] [17] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 during initialization of module PyPlot caused by: PyError (PyImport_ImportModule The Python package matplotlib could not be imported by pyimport. Usually this means that you did not install matplotlib in the Python version being used by PyCall. PyCall is currently configured to use the Julia-specific Python distribution installed by the Conda.jl package. To install the matplotlib module, you can use `pyimport_conda("matplotlib", PKG)`, where PKG is the Anaconda package that contains the module matplotlib, or alternatively you can use the Conda package directly (via `using Conda` followed by `Conda.add` etcetera). Alternatively, if you want to use a different Python distribution on your system, such as a system-wide Python (as opposed to the Julia-specific Python), you can re-configure PyCall with that Python. As explained in the PyCall documentation, set ENV["PYTHON"] to the path/name of the python executable you want to use, run Pkg.build("PyCall"), and re-launch Julia. ) ModuleNotFoundError("No module named 'matplotlib'") Stacktrace: [1] pyimport(name::String) @ PyCall ~/.julia/packages/PyCall/ilqDX/src/PyCall.jl:558 [2] pyimport_conda @ ~/.julia/packages/PyCall/ilqDX/src/PyCall.jl:716 [3] pyimport_conda @ ~/.julia/packages/PyCall/ilqDX/src/PyCall.jl:715 [inlined] [4] __init__() @ PyPlot ~/.julia/packages/PyPlot/H01LC/src/init.jl:173 [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1115 [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}) @ Base ./loading.jl:1061 [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128) @ Base ./loading.jl:1506 [8] _require(pkg::Base.PkgId, env::String) @ Base ./loading.jl:1783 [9] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:1660 [10] macro expansion @ ./loading.jl:1648 [inlined] [11] macro expansion @ ./lock.jl:267 [inlined] [12] require(into::Module, mod::Symbol) @ Base ./loading.jl:1611 ```
Conda info ``` root@30d69add978b:/# /root/.julia/conda/3/x86_64/bin/conda info active environment : None user config file : /root/.condarc populated config files : /root/.julia/conda/3/x86_64/.condarc conda version : 23.7.2 conda-build version : not installed python version : 3.10.12.final.0 virtual packages : __archspec=1=x86_64 __glibc=2.36=0 __linux=5.15.0=0 __unix=0=0 base environment : /root/.julia/conda/3/x86_64 (writable) conda av data dir : /root/.julia/conda/3/x86_64/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /root/.julia/conda/3/x86_64/pkgs /root/.conda/pkgs envs directories : /root/.julia/conda/3/x86_64/envs /root/.conda/envs platform : linux-64 user-agent : conda/23.7.2 requests/2.31.0 CPython/3.10.12 Linux/5.15.0-47-generic debian/12 glibc/2.36 UID:GID : 0:0 netrc file : None offline mode : False ```
Alexander-Barth commented 11 months ago

Other workarounds:

As it is likely a conda problem, I posted this question of StackOverflow: https://stackoverflow.com/questions/76817732/installing-matplotlib-with-conda-fails-with-conda-exceptions-resolvepackagenotfo